The apolipoprotein E (ApoE) locus is expressed in liver, brain and other tissues under the control of cis-acting elements located upstream and downstream from the coding sequence. Recently, an ApoE intron-1 C/G polymorphism has been discovered. We predict that the ApoE intron-1 G allele disrupts the sequence of enhancer elements found to be activated by stress induced transcription factors in other species. The ApoE intron-1 G allele was found strongly linked with the ApoE-epsilon4 allele. The phase of the putative enhancer mutation was such that most epsilon4 alleles would not be activated by stress responses, while about half of the epsilon3 alleles were found to possess the putative stress activated elements. Our working hypothesis is that stress activation of the ApoE-epsilon3 allele would protect from Alzheimer's disease, while stress activation of the ApoE-epsilon4 allele would contribute to Alzheimer's disease risk. This is consistent with evidence that the ApoE*4 protein isoform, which is expressed by the ApoE-epsilon4 allele, interacts aberrantly with brain cellular structures. Previous investigators were not able to determine the haplotype of the combination of ApoE intron-1 C/G ApoE-epsilon3/epsilon4 polymorphisms among double heterozygotes. Using long-range PCR, we will determine the relative risks associated with each of the four ApoE intron-1/ApoE- epsilon haplotypes in double heterozygotes. The relative risk determined from population genetic studies will be compared with the results of our experiments aimed at determining which putative transcription elements actually bind brain expressed transcription factors. Besides the ApoE intron-1 cluster of transcription elements (855 bp), a brain specific element is known to lie between the ApoE and ApoCI genes (5.5 kb). We propose to use mutation scanning techniques to catalogue all polymorphisms that could modulate brain expression of the ApoE locus. We will identify which of the mutations disrupt transcription factor binding and thereby affect relative risk for Alzheimer's disease. These studies should greatly improve Our understanding of how expression of ApoE isoforms affects risks for Alzheimer's disease and may suggest novel strategies for pharmacological intervention.